Jian-Yu Shi

31 papers B 1Journal 26Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
Unlocking molecular optimization potential by leveraging active learning for scaffold-preserving optimization with ALMO.
Expert Syst. Appl.
Zhen-Yi Wu, Peng-Cheng Zhao, Jia-Ning Li, Jian-Yu Shi, Bing-Xue Du
2025 J jnl
Few-shot drug synergy prediction via rapid cross-tier adaptation meta-optimization.
Briefings Bioinform.
Yue-Hua Feng, Ze-Lin Feng, Xiao-Ying Yan, Shao-Wu Zhang, Jian-Yu Shi
2024 J jnl
Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities.
J. Chem. Inf. Model.
Ning-Ning Wang, Bei Zhu, Xin-Liang Li, Shao Liu, Jian-Yu Shi, Dong-Sheng Cao
2024 — conf
DVL-CC: A Novel Dual-View Learning Framework for Compound Cocrystal Prediction Boosted by View Consistency and Complementarity.
BCB
Haoyang Yu, Bei Zhu, Bing-Xue Du, Xue-Xin Wei, Hui Yu, Jian-Yu Shi
2024 J jnl
GGI-DDI: Identification for key molecular substructures by granule learning to interpret predicted drug-drug interactions.
Expert Syst. Appl.
Hui Yu, Jing Wang, Shiyu Zhao, Omayo Silver, Zun Liu, JingTao Yao, Jian-Yu Shi
2024 J jnl
Identifying the reaction centers of molecule based on dual-view representation.
Knowl. Based Syst.
Hui Yu, Jing Wang, Chao Song, Jian-Yu Shi
2024 J jnl
Multi-view clustering with semantic fusion and contrastive learning.
Neurocomputing
Hui Yu, Hui-Xiang Bian, Zi-Ling Chong, Zun Liu, Jian-Yu Shi
2024 J jnl
Prediction of drug-target binding affinity based on multi-scale feature fusion.
Comput. Biol. Medicine
Hui Yu, Wen-Xin Xu, Tian Tan, Zun Liu, Jian-Yu Shi
2024 J jnl
Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation.
Briefings Bioinform.
Guang Yang, Jianing Li, Jinlu Hu, Jian-Yu Shi
2023 J jnl
A social theory-enhanced graph representation learning framework for multitask prediction of drug-drug interactions.
Briefings Bioinform.
Yue-Hua Feng, Shao-Wu Zhang, Yi-Yang Feng, Qing-Qing Zhang, Ming-Hui Shi, Jian-Yu Shi
2023 J jnl
CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning.
Bioinform.
Bing-Xue Du, Yahui Long, Xiaoli Li, Min Wu, Jian-Yu Shi
2023 J jnl
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties.
Bioinform.
Jia-Ning Li, Guang Yang, Peng-Cheng Zhao, Xue-Xin Wei, Jian-Yu Shi
2023 J jnl
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction.
Briefings Bioinform.
Xuan Lin, Lichang Dai, Yafang Zhou, Zu-Guo Yu, Wen Zhang, Jian-Yu Shi, Dong-Sheng Cao, Li Zeng, Haowen Chen, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023 J jnl
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction.
CoRR
Xuan Lin, Lichang Dai, Yafang Zhou, Zu-Guo Yu, Wen Zhang, Jian-Yu Shi, Dong-Sheng Cao, Li Zeng, Haowen Chen, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023 J jnl
Few-Shot Drug Synergy Prediction With a Prior-Guided Hypernetwork Architecture.
IEEE Trans. Pattern Anal. Mach. Intell.
Qing-Qing Zhang, Shaowu Zhang, Yue-Hua Feng, Jian-Yu Shi
2023 — conf
GELKcat: An Integration Learning of Substrate Graph with Enzyme Embedding for Kcat prediction.
BIBM
Bing-Xue Du, Haoyang Yu, Bei Zhu, Yahui Long, Min Wu, Jian-Yu Shi
2023 B conf
MTGL-ADMET: A Novel Multi-task Graph Learning Framework for ADMET Prediction Enhanced by Status-Theory and Maximum Flow.
RECOMB
Bing-Xue Du, Yi Xu, Siu-Ming Yiu, Hui Yu, Jian-Yu Shi
2022 J jnl
Directed graph attention networks for predicting asymmetric drug-drug interactions.
Briefings Bioinform.
Yi-Yang Feng, Hui Yu, Yue-Hua Feng, Jian-Yu Shi
2022 J jnl
Drug-drug interaction prediction with learnable size-adaptive molecular substructures.
Briefings Bioinform.
Arnold K. Nyamabo, Hui Yu, Zun Liu, Jian-Yu Shi
2022 J jnl
MLGL-MP: a Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction.
Bioinform.
Bing-Xue Du, Peng-Cheng Zhao, Bei Zhu, Siu-Ming Yiu, Arnold K. Nyamabo, Hui Yu, Jian-Yu Shi
2022 J jnl
Predict multi-type drug-drug interactions in cold start scenario.
BMC Bioinform.
Zun Liu, Xing-Nan Wang, Hui Yu, Jian-Yu Shi, Wenmin Dong
2021 J jnl
Interpretable prediction of drug-cell line response by triple matrix factorization.
Quant. Biol.
Xiao-Ying Yan, Shaowu Zhang, Siu-Ming Yiu, Jian-Yu Shi
2021 J jnl
SSI-DDI: substructure-substructure interactions for drug-drug interaction prediction.
Briefings Bioinform.
Arnold K. Nyamabo, Hui Yu, Jian-Yu Shi
2020 J jnl
DPDDI: a deep predictor for drug-drug interactions.
BMC Bioinform.
Yue-Hua Feng, Shaowu Zhang, Jian-Yu Shi
2019 J jnl
Detecting drug communities and predicting comprehensive drug-drug interactions via balance regularized semi-nonnegative matrix factorization.
J. Cheminformatics
Jian-Yu Shi, Kui-Tao Mao, Hui Yu, Siu-Ming Yiu
2019 J jnl
Predicting combinative drug pairs via multiple classifier system with positive samples only.
Comput. Methods Programs Biomed.
Jian-Yu Shi, Jia-Xin Li, Kui-Tao Mao, Jiang-Bo Cao, Peng Lei, Hui-Meng Lu, Siu-Ming Yiu
2018 J jnl
Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization.
BMC Syst. Biol.
Hui Yu, Kui-Tao Mao, Jian-Yu Shi, Hua Huang, Zhi Chen, Kai Dong, Siu-Ming Yiu
2018 J jnl
TMFUF: a triple matrix factorization-based unified framework for predicting comprehensive drug-drug interactions of new drugs.
BMC Bioinform.
Jian-Yu Shi, Hua Huang, Jia-Xin Li, Peng Lei, Yan-Ning Zhang, Kai Dong, Siu-Ming Yiu
2017 J jnl
Predicting combinative drug pairs towards realistic screening via integrating heterogeneous features.
BMC Bioinform.
Jian-Yu Shi, Jia-Xin Li, Ke Gao, Peng Lei, Siu-Ming Yiu
2016 — conf
The need of accelerators in analyzing biological networks.
BIBM
Jian-Yu Shi
2010 — conf
Local Phase Quantization Texture Descriptor for Protein Classification.
BIOCOMP
Sheryl Brahnam, Loris Nanni, Jian-Yu Shi, Alessandra Lumini